SDM report

Author

Mårten Erlandsson

Published

2024-03-19

1 Dataset

The models are based on trawling data on the west coast

There are three data sources; IBTS, BITS and NATS

2 Trawl surveys

Information about the trawl surveys…

3 Catches

4 Predictors

  Variables      VIF
1     bTemp 4.043284
2      bSal 2.161882
3     Depth 3.196960
4    botCur 1.307152
5     slope 1.190949
6   fishInt 1.382509
7      maxT 3.904484

5 Presence / Absence models (Biomod2)


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Modeling folder : 
C:/Github Projcects/SDM general scripts/model output/20240910/PA

Species modeled : Plaice

Modeling id : Plaice_2005_2022_AllYear

Considered variables : bTemp bSal Depth botCur slope fishInt maxT


Computed Models :  Plaice_allData_RUN1_GLM Plaice_allData_RUN1_GBM 
Plaice_allData_RUN1_GAM Plaice_allData_RUN1_RF Plaice_allData_RUN1_XGBOOST 
Plaice_allData_RUN2_GLM Plaice_allData_RUN2_GBM Plaice_allData_RUN2_GAM 
Plaice_allData_RUN2_RF Plaice_allData_RUN2_XGBOOST Plaice_allData_allRun_GLM 
Plaice_allData_allRun_GBM Plaice_allData_allRun_GAM Plaice_allData_allRun_RF 
Plaice_allData_allRun_XGBOOST


Failed Models :  none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.ensemble.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=

sp.name : Plaice

expl.var.names : bTemp bSal Depth botCur slope fishInt maxT


models computed: Plaice_EMwmeanByROC_mergedData_mergedRun_mergedAlgo

models failed: none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Modeling folder : 
C:/Github Projcects/SDM general scripts/model output/20240910/PA

Species modeled : Cod

Modeling id : Cod_2005_2022_AllYear

Considered variables : bTemp bSal Depth botCur slope fishInt maxT


Computed Models :  Cod_allData_RUN1_GLM Cod_allData_RUN1_GBM 
Cod_allData_RUN1_GAM Cod_allData_RUN1_RF Cod_allData_RUN1_XGBOOST 
Cod_allData_RUN2_GLM Cod_allData_RUN2_GBM Cod_allData_RUN2_GAM 
Cod_allData_RUN2_RF Cod_allData_RUN2_XGBOOST Cod_allData_allRun_GLM 
Cod_allData_allRun_GBM Cod_allData_allRun_GAM Cod_allData_allRun_RF 
Cod_allData_allRun_XGBOOST


Failed Models :  none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.ensemble.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=

sp.name : Cod

expl.var.names : bTemp bSal Depth botCur slope fishInt maxT


models computed: Cod_EMwmeanByROC_mergedData_mergedRun_mergedAlgo

models failed: none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

6 Abundansmodell (SDM)

class                                 : sdmModels 
======================================================== 
number of species                     :  1 
number of modelling methods           :  3 
names of modelling methods            :  glm, brt, rf 
replicate.methods (data partitioning) :  subsampling 
number of replicates (each method)    :  2 
toral number of replicates per model  :  2 (per species) 
test percentage (in subsampling)      :  25 
------------------------------------------
model run success percentage (per species)  :
------------------------------------------
method          Plaice           
---------------------- 
glm        :        100   %
brt        :        100   %
rf         :        100   %

###################################################################
model Mean performance (per species), using test dataset (generated using partitioning):
-------------------------------------------------------------------------------

 ## species   :  Plaice 
=========================

methods    :     RMSE     |     COR     |     MAE     |     Deviance 
-------------------------------------------------------------------------
glm        :     662.81  |     0.3     |     371.21  |     -558.79  
brt        :     603.64  |     0.34    |     346.85  |     -563.66  
rf         :     814.93  |     0.3     |     408.42  |     -585.78  
```  modelID species method replication replicationID success training test.dep
1       1  Plaice    glm subsampling             1    TRUE     TRUE     TRUE
2       2  Plaice    glm subsampling             2    TRUE     TRUE     TRUE
3       3  Plaice    brt subsampling             1    TRUE     TRUE     TRUE
4       4  Plaice    brt subsampling             2    TRUE     TRUE     TRUE
5       5  Plaice     rf subsampling             1    TRUE     TRUE     TRUE
6       6  Plaice     rf subsampling             2    TRUE     TRUE     TRUE
  test.indep
1      FALSE
2      FALSE
3      FALSE
4      FALSE
5      FALSE
6      FALSE

<simpleError in rep(" ", 7 - length(unlist(strsplit(i, "")))): invalid 'times' argument>
```  modelID species method replication replicationID success training test.dep
1       1     Cod    glm subsampling             1    TRUE     TRUE     TRUE
2       2     Cod    glm subsampling             2    TRUE     TRUE     TRUE
3       3     Cod    brt subsampling             1    TRUE     TRUE     TRUE
4       4     Cod    brt subsampling             2    TRUE     TRUE     TRUE
5       5     Cod     rf subsampling             1    TRUE     TRUE     TRUE
6       6     Cod     rf subsampling             2    TRUE     TRUE     TRUE
  test.indep
1      FALSE
2      FALSE
3      FALSE
4      FALSE
5      FALSE
6      FALSE

7 Validering